[Debian-med-packaging] Bug#951280: ncbi-blast+: runtime trap with at least blastn and makeblastdb

[Patrice DUROUX]

Package: ncbi-blast+
Version: 2.8.1-1
Severity: important

Dear Maintainer,

   * What led up to the situation?

Running commands like one of the following:

blastn -query test.fasta -subject test.fasta

makeblastdb -dbtype nucl -in test.fasta

   * What was the outcome of this action?

A runtime trap with a message 'Instruction non permise'
(sorry for the french message, got the same in a LANG=C env)

Here are extracts from dmesg:

[16975777.040241] traps: blastn[16028] trap invalid opcode ip:7f5c96a4598c sp:7ffece18a380 error:0 in libblast.so[7f5c96a04000+66000]
[16976213.970602] traps: makeblastdb[17484] trap invalid opcode ip:7fca6c0bfb02 sp:7ffe3fae78a0 error:0 in libxutil.so[7fca6c08c000+83000]

and here is the output got using gdb and ncbi-blast+-dbgsym:

gdb --args blastn -query test.fasta -subject test.fasta
GNU gdb (Debian 8.2.1-2+b3) 8.2.1
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
    <http://www.gnu.org/software/gdb/documentation/>.

For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from blastn...Reading symbols from /usr/lib/debug/.build-id/00/382f3290f9ed8c1cace9c6e03d714c031cbd3d.debug...done.
done.
(gdb) go
Command requires an argument.
(gdb) run
Starting program: /usr/bin/blastn -query test.fasta -subject test.fasta

[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
BLASTN 2.8.1+



Program received signal SIGILL, Illegal instruction.
0x00007ffff7afe98c in BLAST_ComputeLengthAdjustment (K=<optimized out>, logK=-0.77652878949899629, alpha_d_lambda=1.171875, beta=-2, 
    query_length=query_length at entry=86, db_length=db_length at entry=86, db_num_seqs=db_num_seqs at entry=1, length_adjustment=length_adjustment at entry=0x7fffffffcf84)
    at ./c++/src/algo/blast/core/blast_stat.c:5093
5093	./c++/src/algo/blast/core/blast_stat.c: No such file or directory.
(gdb) 

The CPU info of the hardware used to run the commands is:

# lscpu
Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
Address sizes:       40 bits physical, 48 bits virtual
CPU(s):              16
On-line CPU(s) list: 0-15
Thread(s) per core:  2
Core(s) per socket:  2
Socket(s):           4
NUMA node(s):        1
Vendor ID:           GenuineIntel
CPU family:          15
Model:               6
Model name:          Intel(R) Xeon(TM) CPU 3.40GHz
Stepping:            8
CPU MHz:             3391.598
BogoMIPS:            6783.19
Virtualization:      VT-x
L1d cache:           16K
L2 cache:            1024K
L3 cache:            16384K
NUMA node0 CPU(s):   0-15
Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc pebs bts nopl cpuid pni dtes64 monitor ds_cpl vmx est tm2 cid cx16 xtpr pdcm lahf_lm pti tpr_shadow vnmi


I hope that is enough information to be helpful.

Thanks,
Patrice


-- System Information:
Debian Release: 10.3
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable-debug'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-5-amd64 (SMP w/16 CPU cores)
Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages ncbi-blast+ depends on:
ii  libbz2-1.0      1.0.6-9.2~deb10u1
ii  libc6           2.28-10
ii  libgcc1         1:8.3.0-6
ii  libgomp1        8.3.0-6
ii  liblmdb0        0.9.22-1
ii  libmbedcrypto3  2.16.0-1
ii  libmbedtls12    2.16.0-1
ii  libpcre3        2:8.39-12
ii  libstdc++6      8.3.0-6
ii  ncbi-data       6.1.20170106+dfsg1-0+deb10u2
ii  perl            5.28.1-6
ii  python          2.7.16-1
ii  zlib1g          1:1.2.11.dfsg-1

ncbi-blast+ recommends no packages.

ncbi-blast+ suggests no packages.

-- no debconf information